A key regulatory loop AK4P1/miR-375/SP1 in pancreatic adenocarcinoma

ABSTRACT Pancreatic adenocarcinoma is one of the leading lethal human cancer types and is notorious for its poor prognosis. A series of bioinformatic analyses and experimental validations were employed to explore the role and mechanism of pseudogene-derived RNAs in pancreatic adenocarcinoma. Consequently, a total of 13 upregulated and 7 downregulated pseudogene-derived RNAs in pancreatic adenocarcinoma were identified. Survival analysis revealed a statistically predictive role of AK4P1 for unfavourable prognosis of patients with pancreatic adenocarcinoma. Subcellular location analysis indicated that AK4P1 was mainly located in cytoplasm, in which AK4P1 might competitively bind to tumour suppressive miR-375 in pancreatic adenocarcinoma. Further analysis showed that SP1 was a potential downstream target gene of miR-375 in pancreatic adenocarcinoma. Intriguingly, expression determination validated that SP1 could positively regulate AK4P1 levels in pancreatic adenocarcinoma. Finally, AK4P1 might also exert its effects by interacting with oncogenic parental gene AK4 in pancreatic adenocarcinoma. Conclusively, the present study elucidated a key regulatory loop AK4P1/miR-375/SP1 in pancreatic adenocarcinoma.


Introduction
Pancreatic adenocarcinoma, the most common type of pancreatic malignancy, ranks the seventh leading cause of cancer-related deaths [1]. During the past decades, a large number of advances in the aspects of diagnosis, preoperation management, surgical treatment, and systematic therapy for pancreatic adenocarcinoma have been achieved [2], the patients with pancreatic adenocarcinoma still possess poor prognosis and rapidly aggress, with nearly 100% of five-year mortality rate [3]. Therefore, it is an urgent need to explore the molecular mechanism and seek effective therapeutic targets or promising prognostic biomarkers in pancreatic adenocarcinoma.
Pseudogene-derived RNAs are a group of noncoding Rs, which play key role in occurrence and progression of human disorders, including cancer [4]. Among all action mechanisms of pseudogenederived RNAs, competing endogenous RNA (ceRNA) hypothesis has been widely acknowledged and reported [5]. For example, Hou et al. suggested that KRT17P3 promoted cisplatin resistance by modulating miR-497-5p/mTOR in non-small cell lung cancer [6]; Zheng et al. indicated that the 3'UTR of CYP4Z2P enhanced tumour angiogenesis of breast cancer by acting as a ceRNA for CYP4Z1 [7]; Zheng et al. demonstrated that pseudogene-derived RNAs were involved in regulation of GJA1 by competitively binding to miR-30d-5p in pancreatic cancer [8]. To date, a systematic study regarding the expression, prognosis, function, and molecular mechanism of pseudogene-derived RNAs in pancreatic adenocarcinoma is still absent and needs to be further elucidated.
In this study, we firstly performed differential expression analysis for pseudogene-derived RNAs in pancreatic adenocarcinoma, then conducted survival analysis for those significant differentiallyexpressed pseudogene-derived RNAs in pancreatic adenocarcinoma and next focused on the molecular mechanism of a pseudogene-derived RNA named AK4P1 in pancreatic adenocarcinoma.

Identification of AK4P1 as a potential pseudogene-derived RNA in PAAD
In order to identify potential pseudogene-derived RNAs in PAAD, dreamBase database was employed. Finally, a total of 621 significant differentially expressed pseudogene-derived RNAs in PAAD were found out, consisting of 258 upregulated and 363 downregulated RNAs (Table S1). To improve the analytic accuracy, GEPIA database was introduced to verify the expression levels of the 621 pseudogene-derived RNAs in PAAD. Among these RNAs, 13 upregulated and 7 downregulated pseudogene-derived RNAs were identified as shown in Figure 1. After performing stage expression analysis, 3 of 20 pseudogene-derived RNAs presented significant expression differences among various major stages in PAAD, involving RP11-719K4.3, FER1L4, and AK4P1 (Table 1 and Figure S1). Subsequently, survival analysis was conducted to assess the prognostic values of the three RNAs in PAAD. Two prognostic indices, consisting of overall survival and disease-free survival, were included. As suggested in Figure 2, among the three RNAs, only high expression of AK4P1 indicated poor overall survival and diseasefree survival in PAAD. Taken together, AK4P1 might be a potential oncogenic RNA molecule and a promising prognostic biomarker in PAAD.

miR-375 is a potential binding miRNA of AK4P1 in PAAD
As previously reported, cytoplasm-located pseudogene-derived RNAs can regulate gene expression by competitively binding to shared miRNAs [5,[8][9][10]. Therefore, we analysed the subcellular location of AK4P1 using lncLocator database. As shown in Figure 3a, AK4P1 was mainly located in cytoplasm, which was followingly validated by nucleo-cytoplasm separation assay (Figure 3b). Subsequently, the downstream miRNAs of AK4P1 were predicted by starBase database. A total of 32 binding miRNAs were found out and a regulatory AK4P1-miRNA network was established using Cytoscape software (Figure 3c). The expression correlation of AK4P1 with the 32 miRNAs was determined ( Table 2). As presented in Figure 3 d and e, only two miRNAs (miR-676-3p and miR-375) were negatively correlated with AK4P1 expression in PAAD. Besides, the prognostic values of miR-676-3p and miR-375 were evaluated by Kaplan-Meier plotter database (figure 3 f and g). The result indicated that PAAD patients with high expression of miR-375 had favourable prognosis, but no significant prognostic predictive role for miR-676-3p in PAAD was observed. These findings suggest that miR-375 might be the most potential downstream binding miRNA of AK4P1 in PAAD.

SP1 is a downstream target gene of miR-375 in PAAD
As widely acknowledged, miRNAs exert their biological roles by negatively modulating gene expression. Therefore, the potential target genes of miR-375 were predicted by miRNet database. To screen out the most potential target genes, only 31 miR-375-target gene pairs that have been validated by reporter assay were included in this study. Based on the action mechanism of miRNA, there should be a negative expression correlation of miR-375 with target genes in PAAD. Thus, correlation analysis was performed by usage of TCGA PAAD data. As listed in Table 3, 16 target genes were significantly inversely correlated with miR-375 in PAAD. Next, survival analysis for the 16 target genes in PAAD was conducted. As suggested in Figure 4 a and b, among the 16 target genes, only increased expression of 12 genes (YAP1, ERBB2, MST1R, YWHAZ, PDK1, CTNNB1, SP1, CIP2A, PIK3CA, PLAG1, MTPN, and MTDH) was positively linked to poor OS and RFS in PAAD. Subsequently, the expression levels of the 12 target genes in PAAD were determined by GEPIA database (Figure 4c-n). Intriguingly, 11 target genes were markedly upregulated in PAAD when compared with normal tissues but no statistical difference of PLAG1 was observed. Correlation analysis revealed that the 11 genes were statistically positively associated with AK4P1 expression in PAAD ( Figure S2). Next, we intended to ascertain if miR-375 could regulate these target  Figure 4o). And by administration of miR-375 inhibitor, among these target genes, only SP1 expression was significantly upregulated in Bxpc.3 ( Figure 4p). Taken these findings into consideration, miR-375 could negatively regulate SP1 expression in PAAD.

Transcription factor SP1 is responsible for AK4P1 overexpression in PAAD
Using online database prediction, 40 transcription factors of AK4P1 were forecasted. Subsequently, expression correlation analysis of AK4P1 with predicted transcription factors was performed (Table  S2). Among these transcription factors, SP1 was significantly positively linked to AK4P1 expression in PAAD, with the correlation coefficient equal to 0.51. Next, we inhibited SP1 expression by transfection of the specific siRNA targeting SP1 in PAAD cell line Bxpc.3 ( Figure 5a). As suggested in Figure 5b, AK4P1 expression was markedly decreased after knockdown of SP1 in PAAD. Intriguingly, knockdown of AK4P1 could also significantly downregulate SP1 protein expression level in PAAD cell ( Figure S3). These results showed that transcription factor SP1 activation might be a key mechanism responsible for AK4P1 upregulation in PAAD.

AK4 is a potential parental gene of AK4P1 in PAAD
Pseudogene-derived RNAs can also exert their roles by positively regulating corresponding parental genes. AK4 is the parental gene of AK4P1. Correlation analysis revealed that AK4 was significantly positively associated with AK4P1 in PAAD (Figure 6a). Moreover, expression analysis indicated a marked upregulation of AK4 in PAAD when compared with normal tissues (Figure 6b). Next, stage expression analysis for AK4 in PAAD was performed. The result showed that the statistical expression difference of AK4 among various stages in PAAD was observed ( Figure 6c). Furthermore, AK4 presented significant prognostic values (overall survival and disease-free survival) in PAAD as suggested in Figure 6 d and e. Moreover, knockdown of AK4P1 could also significantly downregulate AK4 protein expression level in PAAD cell ( Figure S3). Taken together, AK4 is a potential parental gene of AK4P1, and AK4P1 might positively regulate AK4 in PAAD.

Discussion
Pancreatic adenocarcinoma is notorious for its poor prognosis. It makes sense to elucidate the molecular action mechanism of pathogenesis and progression of pancreatic adenocarcinoma.
In this study, we first performed differential expression analysis for pseudogene-derived RNAs in pancreatic adenocarcinoma using dreamBase database, after which GEPIA database was employed to validated those RNAs' expression levels. Consequently, 13 upregulated pseudogenederived RNAs (CTD-3141N22.1, RP11-486A14.1, RP11-719K4.3 et al.) and 7 downregulated pseudogene-derived RNAs (RPL23AP49, USP32P1, RHPXF1P1 et al.) were identified in pancreatic adenocarcinoma. Some of these pseudogenederived RNAs have been reported to be involved in the development and progression of human cancers. For instance, FER1L4 played critical roles in multiple malignancies, including papillary thyroid cancer [11], colorectal cancer [12], liver cancer [13], oral squamous cell carcinoma [14]. Next, stage expression analysis for the 20 RNAs was conducted in pancreatic adenocarcinoma by GEPIA database, and three RNAs (RP11-719K4.3, adenocarcinoma. These findings suggest that AK4P1 might be an oncogenic pseudogenederived RNA and a promising prognostic biomarker in pancreatic adenocarcinoma.  As a type of noncoding RNA, pseudogenederived RNA could exert its effects through competitively binding to shared miRNAs [15,16]. To ascertain if AK4P1 functions by this way in pancreatic adenocarcinoma, first of all, lncLocator tool was used to predict the subcellular location of AK4P1 as previously described [17]. The result, together with the finding from nucleo-cytoplasm separation assay, showed that AK4P1 mainly located in cytoplasm, which provided the suitable place for AK4P1-miRNA binding. Using starBase analysis, 32 miRNAs (miR-28-3p, miR-154-5p, miR-588 et al.) were predicted to potentially bind to AK4P1. Among these miRNAs, only two miRNAs, involving miR-676-3p and miR-375, were inversely correlated with AK4P1 expression in pancreatic adenocarcinoma. Survival analysis showed that miR-375 was a significant favourable prognostic biomarker in pancreatic adenocarcinoma. Lots of studies have demonstrated that miR-375 was a tumour suppressive miRNA in human cancers. For example, miR-375 inhibited progression of hepatocellular carcinoma by targeting JAK2/STAT3 signalling pathway [18]; miR-375 reduced the stemness of gastric cancer cells through triggering ferroptosis [19]; miR-375 also functioned as a tumour suppressor in tongue squamous cell carcinoma [20]. These reports together with our previous analytic results suggested that miR-375 might be a downstream binding miRNA of AK4P1 in pancreatic carcinoma.
Subsequently, we explored the downstream action mechanism of AK4P1/miR-375 in pancreatic adenocarcinoma. It has been widely acknowledged that miRNAs play crucial biological functions by suppressing target gene expression and function [21,22]. By combination of target gene prediction, correlation analysis, survival analysis, and expression determination, a total of 11 potential target genes, involving YAP1, ERBB2, MST1R, YWHAZ, PDK1, CTNNB1, SP1, CIP2A, PIK3CA, PLAG1, MTPN, and MTDH, were screened in pancreatic adenocarcinoma. Among these target genes, only SP1 expression could be negatively regulated by Our team and other groups have validated that pseudogene-derived RNAs could exert their biological effects by alteration of expression and function of parental genes [9,26]. Thus, we explored the relationship between AK4P1 and its parental gene AK4 in pancreatic adenocarcinoma. AK4 has been reported to act as an oncogene in several types of human cancer, including ovarian cancer [27], lung cancer [28,29], HER2-positive breast cancer [30] and bladder cancer [31]. A positive correlation of AK4P1 with AK4 in pancreatic adenocarcinoma was observed. Expression determination, stage expression detection, and survival analysis revealed that AK4 was significantly upregulated in pancreatic carcinoma tissues and its high expression predicted favourable prognosis in pancreatic carcinoma. Moreover, knockdown of AK4P1 could significantly decrease AK4 expression in PAAD. These findings indicated that AK4P1 might positively regulate its parental gene AK4, thereby exerting its roles in pancreatic carcinoma.
In conclusion, the present study elucidated a key regulatory loop AK4P1/miR-375/SP1 in pancreatic carcinoma (Figure 7). Every member in this axis possessed significant values for predicting prognosis of patients with pancreatic adenocarcinoma. Moreover, we also demonstrated that AK4P1 might also exert its oncogenic effects through positively regulating AK4 in pancreatic carcinoma. However, these findings need to be further confirmed by much more experimental validation and clinical trials in the future.

dreamBase analysis
RNA-seq expression data of pseudogene-derived RNAs in human PAAD and normal pancreatic tissues (from TCGA database) were downloaded from the dreamBase database (http://rna.sysu.edu.cn/ dreamBase/index.php) which is a comprehensive platform for analysing modulatory characteristics of pseudogene-derived RNAs from multi-dimensional high-throughput sequencing data [32]. |log 2 (Fold change) (Tumour)|>1.0 was set as the cut-off criterion for identifying differentially expressed pseudogenederived RNA in PAAD. These selected pseudogenederived RNAs were considered as candidate RNAs.
Only miR-375-target gene pairs validated by reporter assay were included for subsequent analysis.

Kaplan-Meier plotter analysis
The prognostic values of miRNAs and target genes in PAAD were assessed using Kaplan-Meier plotter (http://kmplot.com/analysis), which is capable to access the effect of miRNA, gene or protein on survival in more than 20 different cancer types, including PAAD. Logrank P-value <0.05 was considered as statistically significant.

Cell culture
The human PAAD cell line Bxpc.3 was obtained from China Center for Type Culture Collection. Bxpc.3 was cultured in RPMI-1640 (Biological Industries) supplemented with 10% foetal bovine serum (Biological Industries) and placed at 37°C in a humidified incubator containing 5% CO 2 .

Cell transfection
The specific small interfering RNA (siRNA) targeting SP1 (si-SP1) and negative control (si-NC) were designed and synthesized by Guangzhou Ribobio Co. Ltd. (Guangzhou, China). miR-375 mimic, mimic control, inhibitor, and inhibitor control were also obtained from Guangzhou Ribobio Co. Ltd. (Guangzhou, China). Bxpc.3 cells were seeded into six-well plates, after which transfection was performed using Lipofectamine TM 3000 (Invitrogen, Shanghai, China) according to the manufacturer's instruction.

RNA extraction and RT-qPCR
The total RNA was extracted from cells using RNAiso plus Reagent (TaKaRa, Kusatsu, Japan). Then, total RNA was reversely transcribed into complementary DNA (cDNA) by the PrimeScript RT Reagent Kit (TaKaRa, RR0037A). Next, qPCR was conducted using SYBR Premix Ex Taq (TaKaRa, RR420A) in a Roche LightCycler480 II Real-Time PCT Detection System. The gene expression levels relative to GAPDH were analysed using the method of 2 −ddCt .

Western blot analysis
The protein levels of AK4 and SP1 in PAAD cells were determined by normalization to GAPDH as we previously described [39].

Statistical analysis
In this study, most of statistical analyses were performed by corresponding online databases. Besides, experiments were conducted in triplicates and the results were presented as mean ± standard deviation (SD). The experimental statistical analysis was performed using GraphPad Prism Software (Version 7). The differences between two groups were assessed by a two-tailed Student's t-test. P-value <0.05 was considered as statistically significant.